Molecular Oncology, EarlyView.Epithelial–mesenchymal transition (EMT) and tumor‐infiltrating lymphocytes (TILs) are associated with early breast cancer response to neoadjuvant chemotherapy (NAC). This study evaluated EMT and TIL shifts, with immunofluorescence and RNA sequencing, at diagnosis and in residual tumors as potential biomarkers associated with treatment response.
Françoise Derouane +16 more
wiley +1 more source
Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer
Molecular Oncology, EarlyView.We used whole exome and RNA‐sequencing to profile divergent genomic and transcriptomic landscapes of microsatellite stable (MSS) and microsatellite instable (MSI) colorectal cancer. Alterations were classified using a computational score for integrative cancer variant annotation and prioritization.
Efstathios‐Iason Vlachavas +15 more
wiley +1 more source
Towards a core genome: pairwise similarity searches on interspecific genomic data [PDF]
arXiv, 2008 The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional changes going on around them.
arxiv
Detection by complementation of defective or uninducible (herpes simplex type 1) virus genomes latent in human ganglia. [PDF]
, 1979 Stuart M. Brown +4 more
openalex +1 more source
Large-scale discovery of enhancers from human heart tissue. [PDF]
, 2011 Development and function of the human heart depend on the dynamic control of tissue-specific gene expression by distant-acting transcriptional enhancers.
Afzal, Veena +16 more
core
Peripheral blood proteome biomarkers distinguish immunosuppressive features of cancer progression
Molecular Oncology, EarlyView.Immune status significantly influences cancer progression. This study used plasma proteomics to analyze benign 67NR and malignant 4T1 breast tumor models at early and late tumor stages. Immune‐related proteins–osteopontin (Spp1), lactotransferrin (Ltf), calreticulin (Calr) and peroxiredoxin 2 (Prdx2)–were associated with systemic myeloid‐derived ...
Yeon Ji Park +6 more
wiley +1 more source
Zimin patterns in genomes [PDF]
arXivZimin words are words that have the same prefix and suffix. They are unavoidable patterns, with all sufficiently large strings encompassing them. Here, we examine for the first time the presence of k-mers not containing any Zimin patterns, defined hereafter as Zimin avoidmers, in the human genome. We report that in the reference human genome all k-mers
arxiv
TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes [PDF]
arXiv, 2016 Motivation: De Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many genomes of large size (such as mammalian genomes).
arxiv
Epstein-Barr virus and human chromosomes: close association of the resident viral genome and the expression of the virus-determined nuclear antigen (EBNA) with the presence of chromosome 14 in human-mouse hybrid cells. [PDF]
, 1978 Kohtaro Yamamoto +5 more
openalex +1 more source